Each bar shows counts of variant sites removed by the combinations of filters indicated by the dots below.
Variant counts for each strain based on vcf containing all variant sites called by GATK (“soft-filter.vcf”).
Variant count for each strain based on the VCF containing only sites pass all filters (“hard-filter.vcf”). All heterozygous sites on main chromosomes were converted to either homozygous or missing. The remaining heterozygous sites are all located on mitochondria chromosomes.
Number of variants versus the number of heterozygous calls shows strains that might have mixed genotypes or low quality calls (high het but low variation).